flowchart LR
A(Program + Text) -->|knitr| B(Text with\nanalysis results)
B --> C[LaTeX]
C --> CC[PDF]
B --> D[Word]
B --> E[HTML]
B --> F[Presentation]
B --> G[Book]
\(H_0\): The null hypothesis, no effect
\(H_1\): The alternative hypothesis, there is an effect
We run a test, we get a p-value. What is it?
| Frequentist Statistics | Bayesian Statistics |
|---|---|
| 1. Probability is defined as the long-run frequency of events | 1. Probability represents a degree of belief or certainty about an event |
| 2. Parameters (like the “true value”) are fixed but unknown quantities. | 2. Parameters are treated as random variables with their own probability distributions. |
| 3. Asking about the probability of a hypothesis does not make sense | 3. Asking about the probability of a hypothesis is the main goal |
P-values are the language of science, whether we like them (we don’t) or not.
Tip
You have to understand p-values and their limits to talk to other scientists!
flowchart LR
A(Program + Text) -->|knitr| B(Text with\nanalysis results)
B --> C[LaTeX]
C --> CC[PDF]
B --> D[Word]
B --> E[HTML]
B --> F[Presentation]
B --> G[Book]
This can be Rmarkdown, Quarto, Jupyter… the goal is that your code and your text are in one place, and the results of your calculations are entered automatically into the text.
In systems such ar R markdown, you can put directly your analysis results in your text. For example, when I write that the \(p\)-value is equal to 0.05, I am writing this:
In systems such ar R markdown, you can put directly your
analysis results in your text. For example, when I write that the
$p$-value is equal to `r p`, I am writing this:The \(p\)-value above is not entered manually (as 0.05), but is the result of a statistical computation. If the data changes, if your analysis changes, the \(p\)-value above will automatically change as well.
flowchart LR
A(Excel) --> B(Data import)
AA(CSV, TSV) --> B(Data import)
AAA(fastq, ...) --> B(Data import)
B --> C[Data\ncleanup]
C --> D[Long term storage]
C --> E[Analysis]
E --> D
E --> F(Figures)
E --> G(Manuscript\nfragments)
E --> H(Tables\nExcel files)
F --> I[You]
G --> I
H --> I
I --> E
In the diagram above, two things take usually the most hands-on time:
MARCH1 are converted to dates